Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A135 F1 I1 R1 14 200.0 12709596 94.6% 12023277 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,911,972 (T)7→6 intergenic (‑173/‑150) yifB ← / → ilvL predicted bifunctional enzyme and transcriptional regulator/ilvG operon leader peptide

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,911,9660T.98.8% 810.1 / 2.7 162intergenic (‑167/‑156)yifB/ilvLpredicted bifunctional enzyme and transcriptional regulator/ilvG operon leader peptide
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base . (62/98);  total (63/99)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 174 total aligned reads displayed.

AATGATGCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGG  >  REL606/3911892‑3912040
                                                                          |                                                                          
aaTGATGCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAtt                                                                           >  2:1632836/1‑76 (MQ=255)
  tgatgCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAtttt                                                                         >  2:2267962/1‑76 (MQ=255)
  tgatgCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAtttt                                                                         >  1:3660140/1‑76 (MQ=255)
  tgatgCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAtttt                                                                         >  1:5313547/1‑76 (MQ=255)
     tgCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAttttttc                                                                      >  2:3889633/1‑75 (MQ=255)
     tgCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAttttttc                                                                      <  1:2165969/76‑2 (MQ=255)
      gCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAttttttca                                                                     <  2:5836621/76‑3 (MQ=255)
       cTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAttttttcac                                                                    <  1:3084139/76‑4 (MQ=255)
         cGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTtcactc                                                                 >  1:2630082/1‑76 (MQ=255)
          gCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTtcactca                                                                <  2:340623/76‑1 (MQ=255)
          gCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTtcactca                                                                >  1:1983412/1‑76 (MQ=255)
           cAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTtcactcac                                                               <  2:631249/76‑1 (MQ=255)
             aaaaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACta                                                             <  1:5518670/76‑1 (MQ=255)
              aaaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtat                                                            <  1:3826099/76‑1 (MQ=255)
              aaaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtat                                                            <  1:2316641/76‑1 (MQ=255)
               aaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatt                                                           <  1:3870660/76‑1 (MQ=255)
               aaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatt                                                           <  1:3720152/76‑1 (MQ=255)
               aaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatt                                                           <  1:5880961/76‑1 (MQ=255)
                aTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattt                                                          <  2:3172894/76‑1 (MQ=255)
                aTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattt                                                          <  1:4808964/76‑1 (MQ=255)
                 tGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatttt                                                         <  1:2130145/76‑1 (MQ=255)
                 tGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatttt                                                         <  2:292939/76‑1 (MQ=255)
                  gCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatttta                                                        <  1:3357646/76‑1 (MQ=255)
                  gCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatttta                                                        >  1:484082/1‑76 (MQ=255)
                   cAGCGGACAAAGGATGAACTACGAGGAAGGGAGCAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttat                                                       <  1:250350/76‑1 (MQ=255)
                   cAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttat                                                       <  2:687506/76‑1 (MQ=255)
                   cAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttat                                                       <  1:1553841/76‑1 (MQ=255)
                     gCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttattt                                                     <  1:6277586/76‑1 (MQ=255)
                      cGGACAAAGGATGAACTCCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTattttatttt                                                    >  2:1073101/1‑76 (MQ=255)
                      cGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTattttatttt                                                    <  2:3040040/76‑1 (MQ=255)
                      cGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTattttatttt                                                    >  1:2236520/1‑76 (MQ=255)
                        gACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTa                                                  <  1:2991480/76‑1 (MQ=255)
                        gACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTa                                                  >  1:4072280/1‑76 (MQ=255)
                         aCAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaa                                                 <  2:2531164/76‑1 (MQ=255)
                         aCAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaa                                                 <  2:1731760/76‑1 (MQ=255)
                         aCAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaa                                                 <  2:2055446/76‑1 (MQ=255)
                          cAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaa                                                <  1:5952588/76‑1 (MQ=255)
                           aaaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaa                                               >  2:4892593/1‑76 (MQ=255)
                            aaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaa                                              >  2:2068786/1‑76 (MQ=255)
                            aaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaa                                              <  2:412192/76‑1 (MQ=255)
                            aaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaa                                              <  1:1893181/76‑1 (MQ=255)
                            aaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaa                                              <  2:700838/76‑1 (MQ=255)
                             aGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaaa                                             >  2:873201/1‑76 (MQ=255)
                             aGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaaa                                             <  1:2888302/76‑1 (MQ=255)
                             aGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaaa                                             >  1:341153/1‑76 (MQ=255)
                              ggATGAGCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaac                                            <  2:6152396/76‑1 (MQ=255)
                              ggATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaac                                            <  2:4973874/76‑1 (MQ=255)
                              ggATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaac                                            <  1:2888756/76‑1 (MQ=255)
                               gATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaaca                                           <  1:1342173/76‑1 (MQ=255)
                                aTGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaccaa                                          >  2:1443003/1‑76 (MQ=255)
                                aTGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaacaa                                          >  1:3672654/1‑76 (MQ=255)
                                  gAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAacaaca                                        <  2:842694/76‑1 (MQ=255)
                                   aaCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAAcaacaa                                       >  1:5606938/1‑76 (MQ=255)
                                    aCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAt                                      <  1:1809122/76‑1 (MQ=255)
                                      tACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAttt                                    <  1:1059989/76‑1 (MQ=255)
                                      tACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAttt                                    <  1:1737748/76‑1 (MQ=255)
                                      tACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAttt                                    >  1:192553/1‑76 (MQ=255)
                                       aCGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAttt                                    >  1:5057256/1‑76 (MQ=255)
                                       aCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTta                                   >  2:6158367/1‑76 (MQ=255)
                                       aCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTta                                   >  2:5133639/1‑76 (MQ=255)
                                        cGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTtat                                  <  1:556135/76‑1 (MQ=255)
                                        cGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTtat                                  <  2:5170704/76‑1 (MQ=255)
                                          aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTatat                                >  1:6139574/1‑76 (MQ=255)
                                          aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTatat                                >  1:2390366/1‑76 (MQ=255)
                                          aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTatat                                >  1:3417210/1‑76 (MQ=255)
                                            gAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTg                              <  1:4923966/76‑1 (MQ=255)
                                             aaGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGa                             <  1:1264644/76‑1 (MQ=255)
                                             aaGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGa                             <  1:2696928/76‑1 (MQ=255)
                                                  aacaacATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAatta                        >  2:1920519/1‑76 (MQ=255)
                                                    caacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAattatt                      >  2:4741573/1‑76 (MQ=255)
                                                    caacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAattatt                      <  2:2400949/76‑1 (MQ=255)
                                                    caacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAattatt                      <  2:3937895/76‑1 (MQ=255)
                                                    caacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAattatt                      <  2:3256522/76‑1 (MQ=255)
                                                     aacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAAttatta                     >  2:3748191/1‑76 (MQ=255)
                                                     aacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAAttatta                     <  1:3350813/76‑1 (MQ=255)
                                                     aacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAAttatta                     <  1:877477/76‑1 (MQ=255)
                                                     aacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAAttatta                     >  2:4391670/1‑76 (MQ=255)
                                                     aacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAAttatta                     >  2:4572879/1‑76 (MQ=255)
                                                      acaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTaa                    <  2:4303302/76‑1 (MQ=255)
                                                       caTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTaaa                   >  2:3499673/1‑76 (MQ=255)
                                                        aTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAAc                  <  2:2525620/76‑1 (MQ=255)
                                                        aTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAAc                  >  2:5664130/1‑76 (MQ=255)
                                                        aTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAAc                  >  2:1268750/1‑76 (MQ=255)
                                                         ttCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACg                 >  1:935762/1‑76 (MQ=255)
                                                         ttCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACg                 >  1:5613168/1‑76 (MQ=255)
                                                            aTACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcat              <  1:5262217/76‑1 (MQ=255)
                                                               cTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatcat           <  2:4671601/76‑1 (MQ=255)
                                                               cTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatcat           <  1:2679102/76‑1 (MQ=255)
                                                               cTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatcat           <  1:4563643/76‑1 (MQ=255)
                                                                tGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa          >  2:307277/1‑76 (MQ=255)
                                                                tGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa          <  2:6179559/76‑1 (MQ=255)
                                                                tGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa          >  1:933101/1‑76 (MQ=255)
                                                                 gAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaa         >  1:4423387/1‑76 (MQ=255)
                                                                 gAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaa         >  2:301004/1‑76 (MQ=255)
                                                                  aaaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa        <  1:345410/76‑1 (MQ=255)
                                                                  aaaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa        <  1:4396151/76‑1 (MQ=255)
                                                                  aaaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa        <  1:4730334/76‑1 (MQ=255)
                                                                   aaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaaa       <  2:4786098/76‑1 (MQ=255)
                                                                     ttGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAAt     >  1:1086724/1‑76 (MQ=255)
                                                                     ttGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAAt     >  2:4433421/1‑76 (MQ=255)
                                                                          |                                                                          
AATGATGCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGG  >  REL606/3911892‑3912040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A